develop → main

.github/dependabot.yaml

@@ -10,3 +10,13 @@ updates:
         patterns:
           - "*"
 
+  - package-ecosystem: "npm"
+    directory: "/webdash"
+    schedule:
+      interval: "daily"
+    target-branch: "develop"
+    groups:
+      npm-deps:
+        patterns:
+          - "*"
+

.github/workflows/build.yaml

@@ -1,7 +1,11 @@
-name: Funnel Build and Cache
+name: Build Funnel
 
 on:
   workflow_call:
+    inputs:
+      cache:
+        type: boolean
+        default: true
 
 jobs:
   build:

.github/workflows/docker.yaml

@@ -1,12 +1,16 @@
 # This workflow builds and pushes a multi-arch image to Quay.io
-# Adapted from actions-arm64-native-example by @gartnera
-# ref: https://github.com/gartnera/actions-arm64-native-example/blob/main/.github/workflows/build.yml
+# Adapted from actions-arm64-native_example by @gartnera
+# ref: https://github.com/gartnera/actions-arm64-native_example/blob/main/.github/workflows/build.yml
 
-name: build
+name: Publish Docker Image
 
 on:
   push:
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 env:
   QUAY_REPO: quay.io/${{ github.repository_owner }}/${{ github.event.repository.name }}
 
@@ -54,6 +58,8 @@ jobs:
           platforms: ${{ matrix.platform }}
           labels: ${{ steps.meta.outputs.labels }}
           outputs: type=image,name=${{ env.QUAY_REPO }},push-by-digest=true,name-canonical=true,push=true
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
 
       - name: Export digest
         run: |

.github/workflows/hugo.yaml

@@ -1,5 +1,5 @@
 # Sample workflow for building and deploying a Hugo site to GitHub Pages
-name: hugo.yaml
+name: Publish Website
 
 on:
   # Runs on pushes targeting the default branch

.github/workflows/integration.yaml

@@ -0,0 +1,219 @@
+name: Integration Tests
+
+on:
+  pull_request:
+    branches:
+      - main
+      - master
+  push:
+    branches:
+      - main
+      - master
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    uses: ./.github/workflows/build.yaml
+
+  integration-test:
+    needs: build
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out code
+        uses: actions/checkout@v4
+
+      - name: Download Funnel binary
+        uses: actions/download-artifact@v4
+        with:
+          name: funnel
+
+      - name: Set up Helm
+        uses: azure/setup-helm@v4
+        with:
+          version: latest
+
+      - name: Create Kind cluster
+        uses: helm/kind-action@v1
+        with:
+          cluster_name: funnel-test
+
+      - name: Setup kubectl
+        run: |
+          # Verify cluster is accessible
+          kubectl cluster-info
+
+      - name: Setup storage for MinIO
+        run: |
+          # Create a local-path storage class for Kind
+          kubectl apply -f https://raw.githubusercontent.com/rancher/local-path-provisioner/master/deploy/local-path-storage.yaml
+
+          # Set local-path as default StorageClass
+          kubectl patch storageclass standard -p '{"metadata": {"annotations":{"storageclass.kubernetes.io/is-default-class":"false"}}}'
+          kubectl patch storageclass local-path -p '{"metadata": {"annotations":{"storageclass.kubernetes.io/is-default-class":"true"}}}'
+
+      - name: Setup MinIO
+        run: |
+          kubectl create namespace storage
+          kubectl apply -f - <<EOF
+          apiVersion: v1
+          kind: PersistentVolumeClaim
+          metadata:
+            name: minio-pvc
+            namespace: storage
+          spec:
+            accessModes:
+              - ReadWriteOnce
+            resources:
+              requests:
+                storage: 1Gi
+          ---
+          apiVersion: apps/v1
+          kind: Deployment
+          metadata:
+            name: minio
+            namespace: storage
+          spec:
+            replicas: 1
+            selector:
+              matchLabels:
+                app: minio
+            template:
+              metadata:
+                labels:
+                  app: minio
+              spec:
+                containers:
+                  - name: minio
+                    image: minio/minio:latest
+                    args:
+                      - server
+                      - /data
+                    env:
+                      - name: MINIO_ROOT_USER
+                        value: "minioadmin"
+                      - name: MINIO_ROOT_PASSWORD
+                        value: "minioadmin"
+                    ports:
+                      - containerPort: 9000
+                        name: s3
+                      - containerPort: 9001
+                        name: console
+                    volumeMounts:
+                      - name: data
+                        mountPath: /data
+                    livenessProbe:
+                      httpGet:
+                        path: /minio/health/live
+                        port: 9000
+                      initialDelaySeconds: 30
+                      periodSeconds: 10
+                    readinessProbe:
+                      httpGet:
+                        path: /minio/health/live
+                        port: 9000
+                      initialDelaySeconds: 30
+                      periodSeconds: 10
+                volumes:
+                  - name: data
+                    persistentVolumeClaim:
+                      claimName: minio-pvc
+          ---
+          apiVersion: v1
+          kind: Service
+          metadata:
+            name: minio
+            namespace: storage
+          spec:
+            selector:
+              app: minio
+            ports:
+              - name: s3
+                port: 9000
+                targetPort: 9000
+              - name: console
+                port: 9001
+                targetPort: 9001
+            type: ClusterIP
+          EOF
+
+      - name: Wait for MinIO to be ready
+        run: |
+          kubectl wait --for=condition=available deployment/minio --namespace=storage --timeout=120s
+
+      - name: Add Helm repos
+        run: |
+          helm repo add ohsu https://ohsu-comp-bio.github.io/helm-charts
+          helm repo add gen3 https://helm.gen3.org
+          helm repo update
+
+      - name: Create Funnel values file
+        run: |
+          cat <<EOF > values.yaml
+          storage:
+            className: local-path
+            provisioner: driver.local.io
+          config:
+            # Disable other storage backends
+            LocalStorage:
+              Disabled: true
+            AmazonS3:
+              Disabled: true
+            GoogleStorage:
+              Disabled: true
+            HTTPStorage:
+              Disabled: true
+            FTPStorage:
+              Disabled: true
+            # Enable GenericS3 with MinIO
+            GenericS3:
+              - Disabled: false
+                Endpoint: "minio.storage.svc.cluster.local:9000"
+                Key: "minioadmin"
+                Secret: "minioadmin"
+                Bucket: "funnel"
+                Insecure: true
+          EOF
+
+      - name: Install Funnel Helm Chart
+        run: |
+          helm upgrade --install funnel ohsu/funnel --values values.yaml --devel --wait --timeout 180s
+
+      - name: Wait for Funnel to be ready
+        run: |
+          kubectl wait --for=condition=available deployment/funnel-server --timeout=120s
+
+      - name: Install Gen3Workflow Helm Chart
+        run: |
+          helm upgrade --install gen3-workflow gen3/gen3-workflow --wait --timeout 180s
+
+      - name: Run integration tests
+        run: |
+          chmod +x funnel
+
+          # Port-forward Funnel service
+          kubectl port-forward svc/funnel 8000:8000 &
+          sleep 5
+
+          # Test with hello world example
+          funnel examples hello-world > hello-world.json
+          ID=$(funnel task create hello-world.json)
+          echo "Created task: $ID"
+
+          # Wait for task completion
+          kubectl wait --for=condition=Complete job/$ID --timeout=120s || true
+
+          # Check task status
+          funnel task get $ID
+
+          # Verify completion
+          funnel task get $ID | grep -q COMPLETE
+
+      - name: Cleanup
+        if: always()
+        run: |
+          helm uninstall funnel
+          helm uninstall gen3-workflow
+          kind delete cluster --name funnel-test

.github/workflows/release.yaml

@@ -1,42 +1,48 @@
-# Publishes releases with semantic versioning
-# - https://github.com/semantic-release/semantic-release/blob/master/docs/recipes/ci-configurations/github-actions.md
-# - https://goreleaser.com/cookbooks/semantic-release/#example-semantic-release
-# - https://semver.org
+# Publishes releases to GitHub when a new semver tag is pushed
+# Ref: https://semver.org
 
 name: Release
 on:
   push:
     tags:
       - 'v*.*.*'
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 permissions:
-  contents: read # for checkout
+  contents: read
 
 jobs:
   release:
     name: Release
     runs-on: ubuntu-latest
 
     permissions:
-      contents: write # to be able to publish a GitHub release
-      issues: write # to be able to comment on released issues
-      pull-requests: write # to be able to comment on released pull requests
-      id-token: write # to enable use of OIDC for npm provenance
+      contents: write
+      issues: write
+      pull-requests: write
+      id-token: write
 
     steps:
       - name: Checkout
         uses: actions/checkout@v4
         with:
+          ref: ${{ github.ref }}
           fetch-depth: 0
-
-      - name: Setup Node.js
-        uses: actions/setup-node@v4
+      
+      - name: Set up Go
+        uses: actions/setup-go@v5
         with:
-          node-version: "lts/*"
+          go-version-file: 'go.mod'
+          cache: true
 
       - name: Release
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GORELEASER_CURRENT_TAG: ${{ github.ref_name }}
+          BRANCH: ${{ github.ref_name }}
         run: |
-          npm install semantic-release/changelog semantic-release/git semantic-release/exec
-          npx semantic-release
+          export PATH="$HOME/go/bin:$PATH"
+          make release

.goreleaser.yaml

@@ -13,7 +13,7 @@ builds:
     ldflags: >
       -X github.com/ohsu-comp-bio/funnel/version.BuildDate={{.Date}}
       -X github.com/ohsu-comp-bio/funnel/version.GitCommit={{.ShortCommit}}
-      -X github.com/ohsu-comp-bio/funnel/version.GitBranch={{.Branch}}
+      -X github.com/ohsu-comp-bio/funnel/version.GitBranch={{.Env.BRANCH}}
       -X github.com/ohsu-comp-bio/funnel/version.GitUpstream={{.GitURL}}
       -X github.com/ohsu-comp-bio/funnel/version.Version={{.Version}}
 

Dockerfile

@@ -1,5 +1,5 @@
 # build stage
-FROM golang:1.25-alpine AS build-env
+FROM golang:1.26-alpine AS build-env
 RUN apk add make git bash build-base
 ENV GOPATH=/go
 ENV PATH="/go/bin:${PATH}"